| --- |
| license: agpl-3.0 |
| library_name: methscope |
| tags: |
| - dna-methylation |
| - methylation |
| - wgbs |
| - single-cell |
| - imputation |
| - deconvolution |
| - cell-type-annotation |
| --- |
| |
| # MethScope — pretrained models |
|
|
| Pretrained models for [**methscope-cli**](https://github.com/zhou-lab/methscope-cli): |
| ultra-fast analysis of sparse DNA methylomes via MRMP (Most Recurrent Methylation |
| Pattern) encoding. Each model is a **single self-contained bundle** that already |
| carries its MRMP feature definition (and labels / signature), so a query `.cg` |
| runs directly — no separate annotation files. |
|
|
| ## Fetch & run |
|
|
| ```sh |
| # fetch one model (or --local-dir models to grab all) |
| hf download zhou-lab/methscope hg38_celltype.ubjx --local-dir . |
| |
| methscope predict query.cg hg38_celltype.ubjx # cell type / label |
| methscope deconv mixture.cg hg38_65celltypes.refx # cell-type proportions (NNLS) |
| methscope upscale -o out.cg hg38_wg.updecx query.cg # genome-wide CpG upscaling |
| methscope inspect hg38_sex.ubjx # framework, labels, features |
| ``` |
|
|
| Small query `.cg` test fixtures (typed cells, a deconvolution mixture, an |
| upscale input + truth) live in the GitHub repo |
| [`zhou-lab/methscope_data`](https://github.com/zhou-lab/methscope_data) under |
| `test/`, alongside this catalog and the MRMP-construction reproducibility archive. |
|
|
| ## Models |
|
|
| | file | task | framework | labels / notes | |
| |------|------|-----------|----------------| |
| | `hg38_wg.updecx` | whole-genome CpG upscaling | `UPDEC2` | all 29,401,795 hg38 CpGs; the primary upscaler (2.8 GB) | |
| | `hg38_10k1.updecx` | CpG upscaling (single block) | MLP decoder | block 10k1 (10,000 CpGs); small demo model | |
| | `hg38_celltype.ubjx` | cell-type annotation | xgboost | 62 human cell types | |
| | `mm10_celltype.ubjx` | cell-type annotation | xgboost | 41 mouse-brain cell types | |
| | `hg38_sex.ubjx` | sex prediction | logistic | Female, Male (XCI `Xa_hi`/`Xa_lo` markers) | |
| | `hg38_65celltypes.refx` | cell-type deconvolution (NNLS) | refx | 65 types = 58 Zhou + 7 Loyfer organ/blood; split MRMP, 15,300 patterns | |
|
|
| `methscope inspect <model>` prints the exact framework, full label list, and (for |
| linear models) per-feature weights. Classifiers carry a required framework `kind` |
| mark (`xgboost` / `threshold` / `logistic`); `predict` rejects an unmarked |
| bundle. Upscale decoders (`.updecx`) run via `upscale`, deconvolution references |
| (`.refx`, `kind=refx`) via `deconv`. |
|
|
| See the [methscope-cli documentation](https://zhou-lab.github.io/methscope-cli/) |
| for the full command reference and runnable examples. |
|
|
